1
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Sheng G, Li F, Jin W, Wang K. Pan-caner analysis identifies PSMA7 as a targets for amplification at 20q13.33 in tumorigenesis. Sci Rep 2024; 14:3034. [PMID: 38321088 PMCID: PMC10847487 DOI: 10.1038/s41598-024-53585-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 02/02/2024] [Indexed: 02/08/2024] Open
Abstract
The chromosome 20 long arm (20q) is one of the genomic hotspots where copy number alterations frequently occur in multiple types of tumors. However, it remains elusive which genes are implicated in 20q-related tumorigenesis. Here, by querying TCGA and GEO databases, we observed frequent copy number amplification at 20q and the chromosome subband 20q13.33 was amplificated in multiple cancers. Among those genes at 20q13.33, PSMA7 was found with the strongest correlation with cancers. Further analysis revealed that PSMA7 amplification was the most frequent genetic alteration event conferring adverse prognosis in various cancers. Consistent with the strong positive correlation between PSMA7 amplification and gene expression, elevated PSMA7 expression was observed in 20 of 33 types of cancers with a close link to adverse outcomes in certain tumors. In addition, PSMA7 was essential for the growth of almost 1095 cancer lines. Mechanistically, aberrant PSMA7 most probably influenced the proteasome and protease-related pathways to promote tumorigenesis and might be antagonized by several compounds, e.g., Docetaxel in relevant cancers. The current in-depth pan-cancer analysis refines our understanding of the crucial oncogenic role of copy number amplifications at PSMA7 loci at the novel chromosome amplicon 20q13.33 across different tumors.
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Affiliation(s)
- Guangying Sheng
- State Key Laboratory of Medical Genomics, Ruijin Hospital Shanghai Institute of Hematology, National Research Center for Translational Medicine at Shanghai, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Rd, Shanghai, 200025, China
- Ruijin Hospital, Sino-French Research Center for Life Sciences and Genomics, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fuyu Li
- State Key Laboratory of Medical Genomics, Ruijin Hospital Shanghai Institute of Hematology, National Research Center for Translational Medicine at Shanghai, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Rd, Shanghai, 200025, China
- Ruijin Hospital, Sino-French Research Center for Life Sciences and Genomics, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wen Jin
- State Key Laboratory of Medical Genomics, Ruijin Hospital Shanghai Institute of Hematology, National Research Center for Translational Medicine at Shanghai, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Rd, Shanghai, 200025, China
| | - Kankan Wang
- State Key Laboratory of Medical Genomics, Ruijin Hospital Shanghai Institute of Hematology, National Research Center for Translational Medicine at Shanghai, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Rd, Shanghai, 200025, China.
- Ruijin Hospital, Sino-French Research Center for Life Sciences and Genomics, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
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2
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Nejati R, Neumann-Domer R, Liu Z, Koslosky L, Neumann-Domer E, Pei J, Wang YL, Testa JR. Isochromosome 7p, i(7)(p10): A rare AML, myelodysplasia-related entity. Leuk Res Rep 2023; 20:100387. [PMID: 37701905 PMCID: PMC10493252 DOI: 10.1016/j.lrr.2023.100387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 08/25/2023] [Indexed: 09/14/2023] Open
Abstract
We describe genomic findings in an AML case with isochromosome 7p, i(7)(p10), in which SNP array analysis uncovered an additional 7.07-Mb 20q deletion not detected by karyotyping. Several AML cases with i(7)(p10) as an isolated cytogenetic finding have been previously reported. Based on consequent loss of 7q, we propose that AML with i(7)(p10) represents a distinct entity belonging in the WHO group -7/7q-, which represents one of the genetic abnormalities defining AML, myelodysplasia-related. Additionally, the focal del(20q) identified here adds support for a specific common region of deletion in 20q in myeloid malignancies, implicating a small number of candidate genes.
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Affiliation(s)
- Reza Nejati
- Department of Pathology, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA 19111, USA
| | - Ryan Neumann-Domer
- Department of Pathology, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA 19111, USA
- Clinical Cytogenomics Lab, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Zemin Liu
- Department of Pathology, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA 19111, USA
- Clinical Cytogenomics Lab, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Lori Koslosky
- Department of Pathology, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA 19111, USA
- Clinical Cytogenomics Lab, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Erin Neumann-Domer
- Department of Pathology, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA 19111, USA
- Clinical Cytogenomics Lab, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Jianming Pei
- Department of Pathology, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA 19111, USA
- Molecular Diagnostics Lab, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Y. Lynn Wang
- Department of Pathology, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA 19111, USA
- Molecular Diagnostics Lab, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Joseph R. Testa
- Clinical Cytogenomics Lab, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
- Cancer Prevention and Control Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
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3
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Campagna A, De Benedittis D, Fianchi L, Scalzulli E, Rizzo L, Niscola P, Piccioni AL, Di Veroli A, Mancini S, Villivà N, Martini T, Mohamed S, Carmosino I, Criscuolo M, Fenu S, Aloe Spiriti MA, Buccisano F, Mancini M, Tafuri A, Breccia M, Poloni A, Latagliata R. Myelodysplastic Syndromes with Isolated 20q Deletion: A New Clinical-Biological Entity? J Clin Med 2022; 11:2596. [PMID: 35566719 PMCID: PMC9100998 DOI: 10.3390/jcm11092596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 11/16/2022] Open
Abstract
Aims: To define the peculiar features of patients with the deletion of the chromosome 20 long arm (del20q), data from 69 patients with myelodysplastic syndromes (MDSs) and isolated del20q, followed by the Gruppo Romano-Laziale Sindromi Mielodisplastiche (GROM-L) and Ospedale Torrette of Ancona, were collected and compared with those of 502 MDS patients with normal karyotype (NK-MDS). Results: Compared to the NK-MDS group, patients with del20q at diagnosis were older (p = 0.020) and mainly male (p = 0.006). They also had a higher rate of bone marrow blast < 5% (p = 0.004), a higher proportion of low and int-1 risk according to IPSS score (p = 0.023), and lower median platelet (PLT) count (p < 0.001). To date, in the del20q cohort, 21 patients (30.4%) received no treatment, 42 (61.0%) were treated with erythropoiesis-stimulating agents (ESA), 3 (4.3%) with hypomethylating agents, and 3 (4.3%) with other treatments. Among 34 patients evaluable for response to ESA, 21 (61.7%) achieved stable erythroid response according to IWG 2006 criteria and 13 (38.2%) were resistant. Nine patients (13.0%) progressed to acute myeloid leukaemia (AML) after a median time from diagnosis of 28 months (IR 4.1−51.7). The median overall survival (OS) of the entire cohort was 60.6 months (95% CI 54.7−66.4). the 5-year cumulative OS was 55.9% (95% CI 40.6−71.2). Conclusion: According to our results, we hypothesize that MDSs with isolated del 20q may represent a distinct biological entity, with peculiar clinical and prognostic features. The physio-pathological mechanisms underlying the deletion of the chromosome 20 long arm are still unclear and warrant future molecular analysis.
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Affiliation(s)
- Alessia Campagna
- Hematology, Sant’Andrea Hospital, Sapienza University, 00185 Rome, Italy; (A.C.); (M.A.A.S.); (A.T.)
| | - Daniela De Benedittis
- Hematology, Policlinico Umberto I, Sapienza University, 00185 Rome, Italy; (D.D.B.); (E.S.); (L.R.); (S.M.); (I.C.); (M.M.); (M.B.)
| | - Luana Fianchi
- Hematology, Policlinico Gemelli, University of Sacred Heart, 00168 Rome, Italy; (L.F.); (M.C.)
| | - Emilia Scalzulli
- Hematology, Policlinico Umberto I, Sapienza University, 00185 Rome, Italy; (D.D.B.); (E.S.); (L.R.); (S.M.); (I.C.); (M.M.); (M.B.)
| | - Lorenzo Rizzo
- Hematology, Policlinico Umberto I, Sapienza University, 00185 Rome, Italy; (D.D.B.); (E.S.); (L.R.); (S.M.); (I.C.); (M.M.); (M.B.)
| | | | | | | | | | | | - Tiziano Martini
- AOU Ospedali Riuniti, Università Politecnica Marche, 60126 Ancona, Italy; (T.M.); (A.P.)
| | - Sara Mohamed
- Hematology, Policlinico Umberto I, Sapienza University, 00185 Rome, Italy; (D.D.B.); (E.S.); (L.R.); (S.M.); (I.C.); (M.M.); (M.B.)
| | - Ida Carmosino
- Hematology, Policlinico Umberto I, Sapienza University, 00185 Rome, Italy; (D.D.B.); (E.S.); (L.R.); (S.M.); (I.C.); (M.M.); (M.B.)
| | - Marianna Criscuolo
- Hematology, Policlinico Gemelli, University of Sacred Heart, 00168 Rome, Italy; (L.F.); (M.C.)
| | - Susanna Fenu
- Hematology, San Giovanni Hospital, 00184 Rome, Italy; (A.L.P.); (S.F.)
| | | | | | - Marco Mancini
- Hematology, Policlinico Umberto I, Sapienza University, 00185 Rome, Italy; (D.D.B.); (E.S.); (L.R.); (S.M.); (I.C.); (M.M.); (M.B.)
| | - Agostino Tafuri
- Hematology, Sant’Andrea Hospital, Sapienza University, 00185 Rome, Italy; (A.C.); (M.A.A.S.); (A.T.)
| | - Massimo Breccia
- Hematology, Policlinico Umberto I, Sapienza University, 00185 Rome, Italy; (D.D.B.); (E.S.); (L.R.); (S.M.); (I.C.); (M.M.); (M.B.)
| | - Antonella Poloni
- AOU Ospedali Riuniti, Università Politecnica Marche, 60126 Ancona, Italy; (T.M.); (A.P.)
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4
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Macauda A, Giaccherini M, Sainz J, Gemignani F, Sgherza N, Sánchez-Maldonado JM, Gora-Tybor J, Martinez-Lopez J, Carreño-Tarragona G, Jerez A, Spadano R, Gołos A, Jurado M, Hernández-Mohedo F, Mazur G, Tavano F, Butrym A, Várkonyi J, Canzian F, Campa D. Do myeloproliferative neoplasms and multiple myeloma share the same genetic susceptibility loci? Int J Cancer 2020; 148:1616-1624. [PMID: 33038278 DOI: 10.1002/ijc.33337] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 08/04/2020] [Accepted: 08/27/2020] [Indexed: 01/22/2023]
Abstract
Myeloproliferative neoplasms (MPNs) are a group of diseases that cause myeloid hematopoietic cells to overproliferate. Epidemiological and familial studies suggest that genetic factors contribute to the risk of developing MPN, but the genetic susceptibility of MPN is still not well known. Indeed, only few loci are known to have a clear role in the predisposition to this disease. Some studies reported a diagnosis of MPNs and multiple myeloma (MM) in the same patients, but the biological causes are still unclear. We tested the hypothesis that the two diseases share at least partly the same genetic risk loci. In the context of a European multicenter study with 460 cases and 880 controls, we analyzed the effect of the known MM risk loci, individually and in a polygenic risk score (PRS). The most significant result was obtained among patients with chronic myeloid leukemia (CML) for PS0RS1C1-rs2285803, which showed to be associated with an increased risk (OR = 3.28, 95% CI 1.79-6.02, P = .00012, P = .00276 when taking into account multiple testing). Additionally, the PRS showed an association with MPN risk when comparing the last with the first quartile of the PRS (OR = 2.39, 95% CI 1.64-3.48, P = 5.98 × 10-6 ). In conclusion, our results suggest a potential common genetic background between MPN and MM, which needs to be further investigated.
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Affiliation(s)
- Angelica Macauda
- Department of Biology, University of Pisa, Pisa, Italy
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matteo Giaccherini
- Department of Biology, University of Pisa, Pisa, Italy
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Juan Sainz
- Genomic Oncology Area, GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain
- Monoclonal Gammopathies Unit, University Hospital Virgen de las Nieves, Granada, Spain
- Pharmacogenetics Unit, Instituto de Investigación Biosanitaria de Granada (Ibs. Granada), Hospitales Universitarios de Granada/Universidad de Granada, Granada, Spain
- Department of Medicine, University of Granada, Granada, Spain
| | | | - Nicola Sgherza
- Division of Hematology, Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - José Manuel Sánchez-Maldonado
- Pharmacogenetics Unit, Instituto de Investigación Biosanitaria de Granada (Ibs. Granada), Hospitales Universitarios de Granada/Universidad de Granada, Granada, Spain
- Department of Medicine, University of Granada, Granada, Spain
| | | | | | | | - Andrés Jerez
- Hematology and Medical Oncology Department, Hospital Morales Meseguer, IMIB, Murcia, Spain
| | - Raffaele Spadano
- Division of Hematology, Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Aleksandra Gołos
- Department of Clinical Oncology and Chemotherapy, Magodent Hospital, Warsaw, Poland
| | - Manuel Jurado
- Genomic Oncology Area, GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain
- Pharmacogenetics Unit, Instituto de Investigación Biosanitaria de Granada (Ibs. Granada), Hospitales Universitarios de Granada/Universidad de Granada, Granada, Spain
- Department of Medicine, University of Granada, Granada, Spain
| | - Francisca Hernández-Mohedo
- Genomic Oncology Area, GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain
- Pharmacogenetics Unit, Instituto de Investigación Biosanitaria de Granada (Ibs. Granada), Hospitales Universitarios de Granada/Universidad de Granada, Granada, Spain
- Department of Medicine, University of Granada, Granada, Spain
| | - Grzegorz Mazur
- Department of Internal Medicine, Occupational Diseases, Hypertension and Clinical Oncology, Wroclaw Medical University, Wroclaw, Poland
| | - Francesca Tavano
- Division of Gastroenterology and Research Laboratory, Fondazione IRCCS Casa Sollievo della Sofferenza, Foggia, Italy
| | - Aleksandra Butrym
- Department of Cancer Prevention and Therapy, Wroclaw Medical University, Wroclaw, Poland
| | - Judit Várkonyi
- Third Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniele Campa
- Department of Biology, University of Pisa, Pisa, Italy
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5
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SNORA71A Promotes Colorectal Cancer Cell Proliferation, Migration, and Invasion. BIOMED RESEARCH INTERNATIONAL 2020; 2020:8284576. [PMID: 33083486 PMCID: PMC7559222 DOI: 10.1155/2020/8284576] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 09/01/2020] [Accepted: 09/07/2020] [Indexed: 12/24/2022]
Abstract
Small nucleolar RNAs (snoRNAs) play a crucial role during colorectal cancer (CRC) development. The study of SNORA71A is few, and its role in CRC is unknown. This study focused on screening abnormal snoRNAs in CRC and exploring the role of key snoRNA in CRC. The expression pattern of snoRNAs in 3 CRC and 3 normal colon tissues was detected via small RNA sequencing. The six candidate snoRNAs were identified by quantitative PCR (qPCR). Subsequently, the expression level of SNORA71A was further verified through the Cancer Genome Atlas (TCGA) data analysis and qPCR. The CCK8 and transwell assays were used to detect the functional role of SNORA71A in CRC cells. The integrated analysis of snoRNA expression profile indicated that a total 107 snoRNAs were significantly differentially expressed (DE) in CRC tissues compared with normal tissues, including 45 upregulated and 62 downregulated snoRNAs. Bioinformatics analysis revealed that the DE snoRNAs were mainly implicated in "detection of chemical stimulus involved in sensory perception of smell" and "sensory perception of smell" in the biological process. The DE snoRNAs were preferentially enriched in "olfactory transduction" and "glycosphingolipid biosynthesis-ganglio series pathway." The expression of SNORA71A was upregulated in CRC tissues and cells. SNORA71A expression showed statistically significant correlations with TNM stage (P = 0.0196) and lymph node metastasis (P = 0.0189) and can serve as biomarkers for CRC. Importantly, SNORA71A significantly facilitated the CRC cell proliferation, migration, and invasion. Our findings indicate that SNORA71A screened by sequencing acted as an oncogene and promoted proliferation, migration, and invasion ability of CRC cells.
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6
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Nathan S, Bharadwaj S, Luke K, Kalas L, Katz DA, Junaid Hussain M, Miller I, Hsu WT, Shammo J, Venugopal P, Ustun C. Significance of isolated deletion (20q) in donor cells after allogeneic hematopoietic cell transplantation. Leuk Lymphoma 2020; 61:2008-2011. [PMID: 32306813 DOI: 10.1080/10428194.2020.1750609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Sunita Nathan
- Division of Hematology, Oncology and Cellular Therapy, Rush University Medical Center, Chicago, IL, USA
| | - Sushma Bharadwaj
- Division of Hematology and Oncology, John H. Stroger Jr. Hospital of Cook County, Chicago, IL, USA
| | - Kristy Luke
- Division of Hematology, Oncology and Cellular Therapy, Rush University Medical Center, Chicago, IL, USA
| | - Laura Kalas
- Division of Hematology, Oncology and Cellular Therapy, Rush University Medical Center, Chicago, IL, USA
| | - Deborah A Katz
- Division of Hematology, Oncology and Cellular Therapy, Rush University Medical Center, Chicago, IL, USA
| | - Mohammad Junaid Hussain
- Division of Hematology, Oncology and Cellular Therapy, Rush University Medical Center, Chicago, IL, USA
| | - Ira Miller
- Department of Pathology, Rush University Medical Center, Chicago, IL, USA
| | - Wei-Tong Hsu
- Department of Pathology, Rush University Medical Center, Chicago, IL, USA
| | - Jamile Shammo
- Division of Hematology, Oncology and Cellular Therapy, Rush University Medical Center, Chicago, IL, USA
| | - Parameswaran Venugopal
- Division of Hematology, Oncology and Cellular Therapy, Rush University Medical Center, Chicago, IL, USA
| | - Celalettin Ustun
- Division of Hematology, Oncology and Cellular Therapy, Rush University Medical Center, Chicago, IL, USA
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7
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Pure Red Cell Aplasia with Del(20q) Sensitive for Immunosuppressive Treatment. Case Rep Hematol 2020; 2020:1262038. [PMID: 32082654 PMCID: PMC6995481 DOI: 10.1155/2020/1262038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 12/13/2019] [Accepted: 12/28/2019] [Indexed: 11/17/2022] Open
Abstract
Pure red cell aplasia (PRCA) is a rare syndrome that only affects the erythroid lineage. It is defined by a normocytic, normochromic anemia with a marked reticulocytopenia and severe reduction or absence of erythroid precursors in the bone marrow. Treatment of primary, idiopathic PRCA is immunosuppressive therapy. Although it is rare, isolated cytogenetic abnormalities can be seen in PRCA, and abnormal karyotype is associated with poor response to immunosuppressive therapy and poor prognosis. We describe a 77-year-old male with primary, idiopathic PRCA and a deletion of chromosome 20q, del(20q), in the bone marrow cells. He was successfully treated with immunosuppressive therapy and became transfusion-independent. The same cytogenetic abnormality has also been described in a few other reports; taken together, these observations suggest that del(20q) may represent a recurrent cytogenetic abnormality in PRCA. Our case report clearly illustrates that even patients with primary PRCA and an abnormal karyotype can respond to immunosuppression and become transfusion-independent.
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8
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Tang G, Zeng Z, Sun W, Li S, You C, Tang F, Peng S, Ma S, Luo Y, Xu J, Tian X, Zhang N, Gong Y, Xie C. Small Nucleolar RNA 71A Promotes Lung Cancer Cell Proliferation, Migration and Invasion via MAPK/ERK Pathway. J Cancer 2019; 10:2261-2275. [PMID: 31258730 PMCID: PMC6584411 DOI: 10.7150/jca.31077] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 03/14/2019] [Indexed: 12/24/2022] Open
Abstract
Objective: Increasing evidence suggested that dysregulated small nucleolar RNAs (snoRNAs) were involved in tumor development. The roles of snoRNA 71A (SNORA71A) in the progression of non-small cell lung cancer (NSCLC) remained unclear. Methods: Dataset GSE19188 from Gene Expression Omnibus (GEO) database was downloaded to detect the expression levels of SNORA71A in NSCLC tissues. The biological significance of SNORA71A was explored by loss-of-function analysis both in vitro and in vivo. Results: SNORA71A was overexpressed in NSCLC tissues compared with normal tissues, and upregulated SNORA71A was significantly associated with worse survival of NSCLC patients. Knockdown of SNORA71A suppressed proliferation of both A549 and PC9 cells, and induced G0/G1 phase arrest. Knockdown of SNORA71A also suppressed xenograft tumor growth in mice. In addition, knockdown of SNORA71A inhibited cell invasion and migration and suppressed epithelial-mesenchymal transition. Furthermore, downregulated SNORA71A decreased the phosphorylation of MEK and ERK1/2 in the MAPK/ERK signal pathway. Conclusion: SNORA71A functions as an oncogene in NSCLC and may serve as a therapeutic target and promising prognostic biomarker of NSCLC.
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Affiliation(s)
- Guiliang Tang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Zihang Zeng
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Wenjie Sun
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Shuying Li
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Chengcheng You
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Fang Tang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Shan Peng
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Shijing Ma
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Yuan Luo
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Jieyu Xu
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Xiaoli Tian
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Nannan Zhang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Yan Gong
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Conghua Xie
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China.,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China.,Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
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9
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da Silva FB, Machado-Neto JA, Koury LCDA, Bertini VHLL, Ratis CA, Chauffaille MDLLF, Velloso EDRP, Simões BP, Rego EM, Traina F. Acute myeloid leukemia with e1a2 BCR-ABL1 fusion gene: two cases with peculiar molecular and clinical presentations. Rev Bras Hematol Hemoter 2017; 39:379-384. [PMID: 29150116 PMCID: PMC5693268 DOI: 10.1016/j.bjhh.2017.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 06/19/2017] [Accepted: 07/06/2017] [Indexed: 11/21/2022] Open
Affiliation(s)
- Fernanda Borges da Silva
- Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (FMRP USP), Ribeirão Preto, SP, Brazil
| | | | | | | | | | | | - Elvira Deolinda Rodrigues Pereira Velloso
- Hospital Israelita Albert Einstein, São Paulo, SP, Brazil; Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HCFMUSP), São Paulo, SP, Brazil
| | - Belinda Pinto Simões
- Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (FMRP USP), Ribeirão Preto, SP, Brazil
| | - Eduardo Magalhães Rego
- Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (FMRP USP), Ribeirão Preto, SP, Brazil
| | - Fabiola Traina
- Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (FMRP USP), Ribeirão Preto, SP, Brazil.
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10
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Genomic determinants of chronic myelomonocytic leukemia. Leukemia 2017; 31:2815-2823. [PMID: 28555081 DOI: 10.1038/leu.2017.164] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 05/14/2017] [Accepted: 05/19/2017] [Indexed: 12/22/2022]
Abstract
The biology, clinical phenotype and progression rate of chronic myelomonocytic leukemia (CMML) are highly variable due to diverse initiating and secondary clonal genetic events. To determine the effects of molecular features including clonal hierarchy in CMML, we studied whole-exome and targeted next-generation sequencing data from 150 patients with robust clinical and molecular annotation assessed cross-sectionally and at serial time points of disease evolution. To identify molecular lesions unique to CMML, we compared it to the related myeloid neoplasms (N=586), including juvenile myelomonocytic leukemia, myelodysplastic syndromes (MDS) and primary monocytic acute myeloid leukemia and discerned distinct molecular profiles despite similar pathomorphological features. Within CMML, mutations in certain pathways correlated with clinical classification, for example, proliferative vs dysplastic features. While most CMML patients (59%) had ancestral (dominant/co-dominant) mutations involving TET2, SRSF2 or ASXL1 genes, secondary subclonal hierarchy correlated with clinical phenotypes or outcomes. For example, progression was associated with acquisition of new expanding clones carrying biallelic TET2 mutations or RAS family, or spliceosomal gene mutations. In contrast, dysplastic features correlated with mutations usually encountered in MDS (for example, SF3B1 and U2AF1). Classification of CMML based on hierarchies of ancestral and subclonal mutational events may correlate strongly with clinical features and prognosis.
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11
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Song Q, Peng M, Chu Y, Huang S. Techniques for detecting chromosomal aberrations in myelodysplastic syndromes. Oncotarget 2017; 8:62716-62729. [PMID: 28977983 PMCID: PMC5617543 DOI: 10.18632/oncotarget.17698] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 04/19/2017] [Indexed: 11/25/2022] Open
Abstract
Myelodysplastic syndromes (MDS) are a group of heterogeneous hematologic diseases. Chromosomal aberrations are important for the initiation, development, and progression of MDS. Detection of chromosomal abnormalities in MDS is important for categorization, risk stratification, therapeutic selection, and prognosis evaluation of the disease. Recent progress of multiple techniques has brought powerful molecular cytogenetic information to reveal copy number variation, uniparental disomy, and complex chromosomal aberrations in MDS. In this review, we will introduce some common chromosomal aberrations in MDS and their clinical significance. Then we will explain the application, advantages, and limitations of different techniques for detecting chromosomal abnormalities in MDS. The information in this review may be helpful for clinicians to select appropriate methods in patient-related decision making.
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Affiliation(s)
- Qibin Song
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Min Peng
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yuxin Chu
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Shiang Huang
- Molecular department, Kindstar Global, Wuhan, China
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12
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Mosaic chromosome 20q deletions are more frequent in the aging population. Blood Adv 2017; 1:380-385. [PMID: 29296952 DOI: 10.1182/bloodadvances.2016003129] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 01/09/2017] [Indexed: 11/20/2022] Open
Abstract
Deletions on the long-arm of chromosome 20, del(20q), are common karyotypic abnormalities in myeloid disorders. Bioinformatic analyses of the B-allele frequency and log R ratio values from genome-wide association data have identified individuals who are mosaic for large structural abnormalities (>2 Mb). We investigated the most common autosomal event, namely mosaic del(20q), in 46 254 nonhematologic cancer cases and 36 229 cancer-free controls. We detected 91 mosaic del(20q) in leukocytes (80%) and buccal material (20%). The mosaic del(20q) mapped to a well-characterized minimally deleted region (MDR) reported in myeloid disorders. Common breakpoint clusters map to the coordinates of 29.9 to 31.5 Mb on the centromeric side of mosaic del(20q), and 42.0 to 45.4 Mb and 48.1 to 50.7 Mb on the telomeric end (GRCh36). Multivariate analyses suggest del(20q) increases with age, and is more common in males but less common in individuals of African ancestry. No conclusive associations were noted between the presence of mosaic del(20q) and subsequent solid tumor risk. Our observations demonstrate that the MDR of del(20q) is the most common large scale mosaic autosomal abnormality in whole blood and has a frequency of ∼1 in every 1000 adults over the age of 50, which exceeds the expected incidence of myeloid leukemia in the population. Our results indicate that subclonal mosaic events of a region implicated in myeloid disorders on 20q are more frequent than the predicted population-estimated incidence of myeloid diseases, and thus suggest that these events can be tolerated until additional events accumulate that drive myeloid disorders.
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13
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Jobe F, Patel B, Kuzmanovic T, Makishima H, Yang Y, Przychodzen B, Hutchison RE, Bence KK, Maciejewski JP, Mohi G. Deletion of Ptpn1 induces myeloproliferative neoplasm. Leukemia 2017; 31:1229-1234. [PMID: 28111468 DOI: 10.1038/leu.2017.31] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- F Jobe
- Department of Pharmacology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - B Patel
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - T Kuzmanovic
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - H Makishima
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Y Yang
- Department of Pharmacology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - B Przychodzen
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - R E Hutchison
- Department of Pathology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - K K Bence
- Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - J P Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - G Mohi
- Department of Pharmacology, SUNY Upstate Medical University, Syracuse, NY, USA
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14
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Dynamics of clonal evolution in myelodysplastic syndromes. Nat Genet 2016; 49:204-212. [PMID: 27992414 DOI: 10.1038/ng.3742] [Citation(s) in RCA: 310] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 11/16/2016] [Indexed: 12/14/2022]
Abstract
To elucidate differential roles of mutations in myelodysplastic syndromes (MDS), we investigated clonal dynamics using whole-exome and/or targeted sequencing of 699 patients, of whom 122 were analyzed longitudinally. Including the results from previous reports, we assessed a total of 2,250 patients for mutational enrichment patterns. During progression, the number of mutations, their diversity and clone sizes increased, with alterations frequently present in dominant clones with or without their sweeping previous clones. Enriched in secondary acute myeloid leukemia (sAML; in comparison to high-risk MDS), FLT3, PTPN11, WT1, IDH1, NPM1, IDH2 and NRAS mutations (type 1) tended to be newly acquired, and were associated with faster sAML progression and a shorter overall survival time. Significantly enriched in high-risk MDS (in comparison to low-risk MDS), TP53, GATA2, KRAS, RUNX1, STAG2, ASXL1, ZRSR2 and TET2 mutations (type 2) had a weaker impact on sAML progression and overall survival than type-1 mutations. The distinct roles of type-1 and type-2 mutations suggest their potential utility in disease monitoring.
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15
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Jiang MC. CAS (CSE1L) signaling pathway in tumor progression and its potential as a biomarker and target for targeted therapy. Tumour Biol 2016; 37:13077-13090. [PMID: 27596143 DOI: 10.1007/s13277-016-5301-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 08/31/2016] [Indexed: 12/13/2022] Open
Abstract
CSE1L (chromosome segregation 1-like protein), also named as CAS (cellular apoptosis susceptibility protein), is highly expressed in most cancer types. CSE1L/CAS is a multiple functional protein that plays roles in apoptosis, cell survival, chromosome assembly, nucleocytoplasmic transport, microvesicle formation, and cancer metastasis; some of the functions are explicitly correlated. CSE1L is also a cancer serum biomarker. The phosphorylation of CAS is regulated by the extracellular signal-regulated kinase (ERK). The RAS/RAF/MAPK/ERK signaling pathways are the essential targets of most targeted cancer drugs, thus serum phosphorylated CSE1L may be a potential biomarker for monitoring drug resistance in targeted therapy. CSE1L can regulate Ras-induced ERK phosphorylation. CSE1L also regulates the expression and phosphorylation of CREB (cAMP response element binding protein) and MITF (microphthalmia-associated transcription factor) and is thus involved in the melanogenesis and progression of melanoma. CAS is an exosome/microvesicle membrane protein. Tumor cells consistently secrete microvesicles and tumor-derived microvesicles may be accumulated around tumors. Therefore, microvesicle membrane CSE1L may be a potential target for the development of high-efficacy antibody-drug conjugates (ADCs) for cancer therapy. This review will focus on CSE1L expression in cancers, its relationship to Ras/ERK and cAMP/PKA signaling pathways in melanoma development, its potential for the development of ADCs and tumor imaging reagents, and secretory phosphorylated CSE1L for monitoring the emergence of drug resistance in targeted cancer therapy.
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Affiliation(s)
- Ming-Chung Jiang
- Targetrust Biotech. Ltd., No. 510 Zhongzheng Rd, Xinzhuang Dist, New Taipei City, 24205, Taiwan.
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16
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TGF-β induced TMEPAI/PMEPA1 inhibits canonical Smad signaling through R-Smad sequestration and promotes non-canonical PI3K/Akt signaling by reducing PTEN in triple negative breast cancer. Genes Cancer 2014; 5:320-36. [PMID: 25352949 PMCID: PMC4209604 DOI: 10.18632/genesandcancer.30] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 08/25/2014] [Indexed: 01/22/2023] Open
Abstract
TMEPAI (transmembrane prostate androgen-induced) is amplified at genomic, transcript and protein levels in triple-negative breast cancers and promotes TGF-β dependent growth, motility and invasion. Tumor promotion by TMEPAI depends on two different but related actions on TGF-β signaling. Firstly, TMEPAI binds and sequesters regulatory Smads2/3 and thereby decreases growth suppressive signaling by TGF-β. Secondly, increased expression of TMEPAI decreases PTEN (phosphatase and tensin homolog) abundance, and thereby increases TGF-β dependent tumor promotive PI3K/Akt signaling. These actions of TMEPAI give rise to increased cell proliferation and motility. Moreover, signaling alterations produced by high TMEPAI were associated with oncogenic Snail expression and lung metastases. Finally, an inverse correlation between TMEPAI and PTEN levels was confirmed in triple negative breast cancer tumor samples. Together, our findings suggest that TMEPAI has dually critical roles to promote TGF-β dependent cancer cell growth and metastasis. Thus, redirected TGF-β signaling through TMEPAI may play a pivotal role in TGF-β mediated tumor promotion.
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Iacobucci I, Lonetti A, Papayannidis C, Martinelli G. Use of single nucleotide polymorphism array technology to improve the identification of chromosomal lesions in leukemia. Curr Cancer Drug Targets 2014; 13:791-810. [PMID: 23941516 PMCID: PMC4104470 DOI: 10.2174/15680096113139990089] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 04/05/2013] [Accepted: 07/01/2013] [Indexed: 12/13/2022]
Abstract
Acute leukemias are characterized by recurring chromosomal and genetic abnormalities that disrupt normal development and drive aberrant cell proliferation and survival. Identification of these abnormalities plays important role in diagnosis, risk assessment and patient classification. Until the last decade methods to detect these aberrations have included genome wide approaches, such as conventional cytogenetics, but with a low sensitivity (5-10%), or gene candidate approaches, such as fluorescent in situ hybridization, having a greater sensitivity but being limited to only known regions of the genome. Single nucleotide polymorphism (SNP) technology is a screening method that has revolutionized our way to find genetic alterations, enabling linkage and association studies between SNP genotype and disease as well as the identification of alterations in DNA content on a whole genome scale. The adoption of this approach for the study of lymphoid and myeloid leukemias contributed to the identification of novel genetic alterations, such as losses/gains/uniparental disomy not visible by cytogenetics and implicated in pathogenesis, improving risk assessment and patient classification and in some cases working as targets for tailored therapies. In this review, we reported recent advances obtained in the knowledge of the genomic complexity of chronic myeloid leukemia and acute leukemias thanks to the use of high-throughput technologies, such as SNP array.
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Affiliation(s)
- Ilaria Iacobucci
- Institute of Hematology "L. e A. Seràgnoli" Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy, Via Massarenti, 9 - 40138 Bologna, Italy.
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18
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Durable hematological and major cytogenetic response in a patient with isolated 20q deletion myelodysplastic syndrome treated with lenalidomide. Case Rep Oncol Med 2014; 2014:949515. [PMID: 24716056 PMCID: PMC3970358 DOI: 10.1155/2014/949515] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 12/31/2013] [Indexed: 11/17/2022] Open
Abstract
Myelodysplastic syndrome (MDS) is a clonal bone marrow disorder characterized by ineffective hematopoiesis. It is characterized by peripheral blood cytopenia and significant risk of progression to acute myeloid leukemia result. Deletion of the long arm of chromosome 20 (20q deletion) is present in 3–7% of patients with MDS. Lenalidomide is an immunomodulatory agent with antiangiogenic activity. It is FDA approved for the treatment of anemia in patients with low or int-1 risk MDS with chromosome 5q deletion with or without additional cytogenetic abnormalities. Study of lenalidomide in patients with MDS without 5q deletion but other karyotypic abnormalities demonstrated meaningful activity in transfusion dependent patients; however, response of patients with isolated 20q deletion to lenalidomide is not known. We are reporting a patient with 20q deletion MDS treated with lenalidomide after he failed to respond to azacytidine; to our knowledge this is the first report of a patient with isolated 20q deletion treated with lenalidomide.
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Valli R, Pressato B, Marletta C, Mare L, Montalbano G, Curto FL, Pasquali F, Maserati E. Different loss of material in recurrent chromosome 20 interstitial deletions in Shwachman-Diamond syndrome and in myeloid neoplasms. Mol Cytogenet 2013; 6:56. [PMID: 24330778 PMCID: PMC3914702 DOI: 10.1186/1755-8166-6-56] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 11/04/2013] [Indexed: 12/19/2022] Open
Abstract
Background An interstitial deletion of the long arms of chromosome 20, del(20)(q), is frequent in the bone marrow (BM) of patients with myelodysplastic syndromes (MDS), acute myeloid leukemia (AML), and myeloproliferative neoplasms (MPN), and it is recurrent in the BM of patients with Shwachman-Diamond syndrome (SDS), who have a 30-40% risk of developing MDS and AML. Results We report the results obtained by microarray-based comparative genomic hybridization (a-CGH) in six patients with SDS, and we compare the loss of chromosome 20 material with one patient with MDS, and with data on 92 informative patients with MDS/AML/MPN and del(20)(q) collected from the literature. Conclusions The chromosome material lost in MDS/AML/MPN is highly variable with no identifiable common deleted regions, whereas in SDS the loss is more uniform: in 3/6 patients it was almost identical, and the breakpoints that we defined are probably common to most patients from the literature. In some SDS patients less material may be lost, due to different distal breakpoints, but the proximal breakpoint is in the same region, always leading to the loss of the EIF6 gene, an event which was related to a lower risk of MDS/AML in comparison with other patients.
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Affiliation(s)
| | | | | | | | | | | | | | - Emanuela Maserati
- Dipartimento di Medicina Clinica e Sperimentale, Università dell'Insubria, Via J, H, Dunant, 5, I 21100 Varese, Italy.
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20
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Heinrichs S, Conover LF, Bueso-Ramos CE, Kilpivaara O, Stevenson K, Neuberg D, Loh ML, Wu WS, Rodig SJ, Garcia-Manero G, Kantarjian HM, Look AT. MYBL2 is a sub-haploinsufficient tumor suppressor gene in myeloid malignancy. eLife 2013; 2:e00825. [PMID: 23878725 PMCID: PMC3713455 DOI: 10.7554/elife.00825] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 06/14/2013] [Indexed: 01/12/2023] Open
Abstract
A common deleted region (CDR) in both myelodysplastic syndromes (MDS) and myeloproliferative neoplasms (MPN) affects the long arm of chromosome 20 and has been predicted to harbor a tumor suppressor gene. Here we show that MYBL2, a gene within the 20q CDR, is expressed at sharply reduced levels in CD34+ cells from most MDS cases (65%; n = 26), whether or not they harbor 20q abnormalities. In a murine competitive reconstitution model, Mybl2 knockdown by RNAi to 20-30% of normal levels in multipotent hematopoietic progenitors resulted in clonal dominance of these 'sub-haploinsufficient' cells, which was reflected in all blood cell lineages. By 6 months post-transplantation, the reconstituted mice had developed a clonal myeloproliferative/myelodysplastic disorder originating from the cells with aberrantly reduced Mybl2 expression. We conclude that downregulation of MYBL2 activity below levels predicted by classical haploinsufficiency underlies the clonal expansion of hematopoietic progenitors in a large fraction of human myeloid malignancies. DOI:http://dx.doi.org/10.7554/eLife.00825.001.
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Affiliation(s)
- Stefan Heinrichs
- Institute of Transfusion Medicine , University Hospital Essen , Essen , Germany ; Department of Pediatric Oncology , Dana-Farber Cancer Institute , Boston , United States
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21
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Shaffer LG, Ballif BC, Schultz RA. The use of cytogenetic microarrays in myelodysplastic syndrome characterization. Methods Mol Biol 2013; 973:69-85. [PMID: 23412784 DOI: 10.1007/978-1-62703-281-0_5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Various microarray platforms, including BAC, oligonucleotide, and SNP arrays, have been shown to -provide clinically useful diagnostic and prognostic information for patients with myelodysplastic syndromes (MDS). Clinically useful arrays are designed with specific purposes in mind and with attention to genomic content and probe density. All array types have been shown to detect genomic copy gains and losses, with SNP arrays having the added advantage of detecting copy neutral loss of heterozygosity (CNLOH). The finding of CNLOH has led to the identification of certain disease genes implicated in the initiation or progression of myeloid diseases. In addition, SNP karyotyping alone, or in conjunction with routine cytogenetics, can affect the outcome prediction and improve prognostic stratification of patients with MDS. Patients who were reclassified after array testing as having adverse-risk chromosomal findings correlated with poor survival. Results of over 25 published studies support the use of arrays in MDS testing. Because few balanced translocations are found in MDS, this disease is particularly amenable to microarray testing, and studies have shown better disease classification, identification of cryptic changes, and prognostication in this heterogeneous group of disorders. Novel genomic alterations identified by array testing may lead to better targeted therapies for treating patients with MDS.
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Affiliation(s)
- Lisa G Shaffer
- Signature Genomic Laboratories, PerkinElmer Inc., Spokane, WA, USA.
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22
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Hahm C, Mun YC, Seong CM, Chung WS, Huh J. Additional genomic aberrations identified by single nucleotide polymorphism array-based karyotyping in an acute myeloid leukemia case with isolated del(20q) abnormality. Ann Lab Med 2012; 32:445-9. [PMID: 23130347 PMCID: PMC3486942 DOI: 10.3343/alm.2012.32.6.445] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 08/13/2012] [Accepted: 09/20/2012] [Indexed: 11/19/2022] Open
Abstract
Prognosis is known to be better in cases with isolated chromosomal abnormalities than in those with complex karyotypes. Accordingly, del(20q) as an isolated abnormality must be distinguished from cases in which it is associated with other chromosomal rearrangements for a better stratification of prognosis. We report a case of an isolated del(20q) abnormality with additional genomic aberrations identified using whole-genome single nucleotide polymorphism array (SNP-A)-based karyotyping. A 39-yr-old man was diagnosed with AML without maturation. Metaphase cytogenetic analysis (MC) revealed del(20)(q11.2) as the isolated abnormality in 100% of metaphase cells analyzed, and FISH analysis using D20S108 confirmed the 20q deletion in 99% of interphase cells. Using FISH, other rearrangements such as BCR/ABL1, RUNX1/RUNX1T1, PML/RARA, CBFB/MYH11, and MLL were found to be negative. SNP-A identified an additional copy neutral loss of heterozygosity (CN-LOH) in the 11q13.1-q25 region. Furthermore, SNP-A allowed for a more precise definition of the breakpoints of the 20q deletion (20q11.22-q13.31). Unexpectedly, the terminal regions showed gain on chromosome 20q. The patient did not achieve complete remission; 8 months later, he died from complications of leukemic cell infiltrations into the central nervous system. This study suggests that a presumably isolated chromosomal abnormality by MC may have additional genomic aberrations, including CN-LOH, which could be associated with a poor prognosis. SNP-A-based karyotyping may be helpful for distinguishing true isolated cases from cases in combination with additional genomic aberrations not detected by MC.
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Affiliation(s)
- Chorong Hahm
- Department of Laboratory Medicine, Ewha Womans University School of Medicine, Seoul, Korea
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23
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Traina F, Visconte V, Jankowska AM, Makishima H, O’Keefe CL, Elson P, Han Y, Hsieh FH, Sekeres MA, Mali RS, Kalaycio M, Lichtin AE, Advani AS, Duong HK, Copelan E, Kapur R, Olalla Saad ST, Maciejewski JP, Tiu RV. Single nucleotide polymorphism array lesions, TET2, DNMT3A, ASXL1 and CBL mutations are present in systemic mastocytosis. PLoS One 2012; 7:e43090. [PMID: 22905207 PMCID: PMC3419680 DOI: 10.1371/journal.pone.0043090] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 07/17/2012] [Indexed: 01/08/2023] Open
Abstract
We hypothesized that analysis of single nucleotide polymorphism arrays (SNP-A) and new molecular defects may provide new insight in the pathogenesis of systemic mastocytosis (SM). SNP-A karyotyping was applied to identify recurrent areas of loss of heterozygosity and bidirectional sequencing was performed to evaluate the mutational status of TET2, DNMT3A, ASXL1, EZH2, IDH1/IDH2 and the CBL gene family. Overall survival (OS) was analyzed using the Kaplan-Meier method. We studied a total of 26 patients with SM. In 67% of SM patients, SNP-A karyotyping showed new chromosomal abnormalities including uniparental disomy of 4q and 2p spanning TET2/KIT and DNMT3A. Mutations in TET2, DNMT3A, ASXL1 and CBL were found in 23%, 12%, 12%, and 4% of SM patients, respectively. No mutations were observed in EZH2 and IDH1/IDH2. Significant differences in OS were observed for SM mutated patients grouped based on the presence of combined TET2/DNMT3A/ASXL1 mutations independent of KIT (P = 0.04) and sole TET2 mutations (P<0.001). In conclusion, TET2, DNMT3A and ASXL1 mutations are also present in mastocytosis and these mutations may affect prognosis, as demonstrated by worse OS in mutated patients.
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Affiliation(s)
- Fabiola Traina
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
- Hematology and Hemotherapy Center, INCT do Sangue, University of Campinas, Campinas, São Paulo, Brazil
| | - Valeria Visconte
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Anna M. Jankowska
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Hideki Makishima
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Christine L. O’Keefe
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Paul Elson
- Department of Quantitative Health Sciences, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Yingchun Han
- Department of Pathobiology, Lerner Research Institute and Allergy and Immunology, Respiratory Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Fred H. Hsieh
- Department of Pathobiology, Lerner Research Institute and Allergy and Immunology, Respiratory Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Mikkael A. Sekeres
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
- Department of Hematologic Oncology and Blood Disorders, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Raghuveer Singh Mali
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University of School of Medicine, Indianapolis, Indiana, United States of America
| | - Matt Kalaycio
- Department of Hematologic Oncology and Blood Disorders, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Alan E. Lichtin
- Department of Hematologic Oncology and Blood Disorders, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Anjali S. Advani
- Department of Hematologic Oncology and Blood Disorders, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Hien K. Duong
- Department of Hematologic Oncology and Blood Disorders, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Edward Copelan
- Department of Hematologic Oncology and Blood Disorders, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Reuben Kapur
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University of School of Medicine, Indianapolis, Indiana, United States of America
| | - Sara T. Olalla Saad
- Hematology and Hemotherapy Center, INCT do Sangue, University of Campinas, Campinas, São Paulo, Brazil
| | - Jaroslaw P. Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
- Department of Hematologic Oncology and Blood Disorders, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Ramon V. Tiu
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
- Department of Hematologic Oncology and Blood Disorders, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
- * E-mail:
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24
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Jerez A, Gondek LP, Jankowska AM, Makishima H, Przychodzen B, Tiu RV, O'Keefe CL, Mohamedali AM, Batista D, Sekeres MA, McDevitt MA, Mufti GJ, Maciejewski JP. Topography, clinical, and genomic correlates of 5q myeloid malignancies revisited. J Clin Oncol 2012; 30:1343-9. [PMID: 22370328 DOI: 10.1200/jco.2011.36.1824] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Interstitial deletions of chromosome 5q are common in acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS), pointing toward the pathogenic role of this region in disease phenotype and clonal evolution. The higher level of resolution of single-nucleotide polymorphism array (SNP-A) karyotyping may be used to find cryptic abnormalities and to precisely define the topographic features of the genomic lesions, allowing for more accurate clinical correlations. PATIENTS AND METHODS We analyzed high-density SNP-A karyotyping at diagnosis for a cohort of 1,155 clinically well-annotated patients with malignant myeloid disorders. results: We identified chromosome 5q deletions in 142 (12%) of 1,155 patients and uniparental disomy segments (UPD) in four (0.35%) of 1,155 patients. Patients with deletions involving the centromeric and telomeric extremes of 5q have a more aggressive disease phenotype and additional chromosomal lesions. Lesions not involving the centromeric or telomeric extremes of 5q are not exclusive to 5q- syndrome but can be associated with other less aggressive forms of MDS. In addition, larger 5q deletions are associated with either del(17p) or UPD17p. In 31 of 33 patients with del(5q) AML, either a deletion involving the centromeric and/or telomeric regions or heterozygous mutations in NPM1 or MAML1 located in 5q35 were present. CONCLUSION Our results suggest that the extent of the affected region on 5q determines clinical characteristics that can be further modified by heterozygous mutations present in the telomeric extreme.
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Nikoloski G, van der Reijden BA, Jansen JH. Mutations in epigenetic regulators in myelodysplastic syndromes. Int J Hematol 2012; 95:8-16. [PMID: 22234528 DOI: 10.1007/s12185-011-0996-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2011] [Accepted: 12/12/2011] [Indexed: 12/15/2022]
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SNPs array karyotyping reveals a novel recurrent 20p13 amplification in primary myelofibrosis. PLoS One 2011; 6:e27560. [PMID: 22110671 PMCID: PMC3215741 DOI: 10.1371/journal.pone.0027560] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Accepted: 10/19/2011] [Indexed: 01/22/2023] Open
Abstract
The molecular pathogenesis of primary mielofibrosis (PMF) is still largely unknown. Recently, single-nucleotide polymorphism arrays (SNP-A) allowed for genome-wide profiling of copy-number alterations and acquired uniparental disomy (aUPD) at high-resolution. In this study we analyzed 20 PMF patients using the Genome-Wide Human SNP Array 6.0 in order to identify novel recurrent genomic abnormalities. We observed a complex karyotype in all cases, detecting all the previously reported lesions (del(5q), del(20q), del(13q), +8, aUPD at 9p24 and abnormalities on chromosome 1). In addition, we identified several novel cryptic lesions. In particular, we found a recurrent alteration involving cytoband 20p13 in 55% of patients. We defined a minimal affected region (MAR), an amplification of 9,911 base-pair (bp) overlapping the SIRPB1 gene locus. Noteworthy, by extending the analysis to the adjacent areas, the cytoband was overall affected in 95% of cases. Remarkably, these results were confirmed by real-time PCR and validated in silico in a large independent series of myeloproliferative diseases. Finally, by immunohistochemistry we found that SIRPB1 was over-expressed in the bone marrow of PMF patients carrying 20p13 amplification. In conclusion, we identified a novel highly recurrent genomic lesion in PMF patients, which definitely warrant further functional and clinical characterization.
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Stein BL, Williams DM, O'Keefe C, Rogers O, Ingersoll RG, Spivak JL, Verma A, Maciejewski JP, McDevitt MA, Moliterno AR. Disruption of the ASXL1 gene is frequent in primary, post-essential thrombocytosis and post-polycythemia vera myelofibrosis, but not essential thrombocytosis or polycythemia vera: analysis of molecular genetics and clinical phenotypes. Haematologica 2011; 96:1462-9. [PMID: 21712540 DOI: 10.3324/haematol.2011.045591] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND The myeloproliferative neoplasms, essential thrombocytosis, polycythemia vera and primary myelofibrosis, share the same acquired genetic lesion, but the concept of JAK2 V617F serving as the sole lesion responsible for these neoplasms is under question, and there has been interest in identifying additional mutations that may contribute to disease pathogenesis. Because ASXL1 lesions have been increasingly identified in myeloid neoplasms, we examined the relationships of ASXL1 mutation or deletion to both clinical phenotype and associated molecular features in 166 patients with myeloproliferative neoplasms. DESIGN AND METHODS Exon 12 of ASXL1 was amplified from neutrophil genomic DNA and bidirectionally sequenced in 77 patients with myelofibrosis (including patients with primary and post-essential thrombocytosis or post-polycythemia myelofibrosis), 42 patients with polycythemia vera, 41 with essential thrombocytosis and 6 with post-myelofibrosis acute myeloid leukemia. Pyrosequencing assays were designed to determine the allele percentages of JAK2 V617F (G5073770T), ASXL1 2475dupA, and ASXL1 2846_2847del in neutrophil genomic DNA samples. Clinical and laboratory characteristics of patients with wild-type and ASXL1 mutations were then compared. RESULTS We identified nonsense mutations or hemizygous deletion of ASXL1 in 36% of the patients with myelofibrosis, but very rarely among those with polycythemia vera or essential thrombocytosis. Among the patients with myelofibrosis, those with ASXL1 lesions were not distinguished from their wild-type counterparts with regard to JAK2 V617F status, exposure to chemotherapy or evolution to leukemia. Myelofibrosis patients with ASXL1 lesions were more likely to have received anemia-directed therapy compared to those without lesions [15/26 (58%) versus 11/39 (23%); P=0.02]. Using serial banked samples and quantitative ASXL1 mutant allele burden assays, we observed the acquisition and accumulation of ASXL1 mutations over time in two patients with post-essential thrombocytosis myelofibrosis. CONCLUSIONS ASXL1 haploinsufficiency is associated with a myelofibrosis phenotype in the context of other known and unknown lesions, and disruption of ASXL1 function may contribute to the disease pathogenesis of myelofibrosis.
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Affiliation(s)
- Brady L Stein
- Medicine, Northwestern University Feinberg School of Medicine, USA
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Godley LA, Cunningham J, Dolan ME, Huang RS, Gurbuxani S, McNerney ME, Larson RA, Leong H, Lussier Y, Onel K, Odenike O, Stock W, White KP, Le Beau MM. An integrated genomic approach to the assessment and treatment of acute myeloid leukemia. Semin Oncol 2011; 38:215-24. [PMID: 21421111 DOI: 10.1053/j.seminoncol.2011.01.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Traditionally, new scientific advances have been applied quickly to the leukemias based on the ease with which relatively pure samples of malignant cells can be obtained. Currently, our arsenal of approaches used to characterize an individual's acute myeloid leukemia (AML) combines hematopathologic evaluation, flow cytometry, cytogenetic analysis, and molecular studies focused on a few key genes. The advent of high-throughput methods capable of full-genome evaluation presents new options for a revolutionary change in the way we diagnose, characterize, and treat AML. Next-generation DNA sequencing techniques allow full sequencing of a cancer genome or transcriptome, with the hope that this will be affordable for routine clinical care within the decade. Microarray-based testing will define gene and miRNA expression, DNA methylation patterns, chromosomal imbalances, and predisposition to disease and chemosensitivity. The vision for the future entails an integrated and automated approach to these analyses, bringing the possibility of formulating an individualized treatment plan within days of a patient's initial presentation. With these expectations comes the hope that such an approach will lead to decreased toxicities and prolonged survival for patients.
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Affiliation(s)
- Lucy A Godley
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA. lgodley@medicine
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CBL, CBLB, TET2, ASXL1, and IDH1/2 mutations and additional chromosomal aberrations constitute molecular events in chronic myelogenous leukemia. Blood 2011; 117:e198-206. [PMID: 21346257 DOI: 10.1182/blood-2010-06-292433] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Progression of chronic myelogenous leukemia (CML) to accelerated (AP) and blast phase (BP) is because of secondary molecular events, as well as additional cytogenetic abnormalities. On the basis of the detection of JAK2, CBL, CBLB, TET2, ASXL1, and IDH1/2 mutations in myelodysplastic/myeloproliferative neoplasms, we hypothesized that they may also contribute to progression in CML. We screened these genes for mutations in 54 cases with CML (14 with chronic phase, 14 with AP, 20 with myeloid, and 6 with nonmyeloid BP). We identified 1 CBLB and 2 TET2 mutations in AP, and 1 CBL, 1 CBLB, 4 TET2, 2 ASXL1, and 2 IDH family mutations in myeloid BP. However, none of these mutations were found in chronic phase. No cases with JAK2V617F mutations were found. In 2 cases, TET2 mutations were found concomitant with CBLB mutations. By single nucleotide polymorphism arrays, uniparental disomy on chromosome 5q, 8q, 11p, and 17p was found in AP and BP but not involving 4q24 (TET2) or 11q23 (CBL). Microdeletions on chromosomes 17q11.2 and 21q22.12 involved tumor associated genes NF1 and RUNX1, respectively. Our results indicate that CBL family, TET2, ASXL1, and IDH family mutations and additional cryptic karyotypic abnormalities can occur in advanced phase CML.
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